You set in the header.tpl a BIG FIXME on the paths to CSS. But why???
You set a T_STYLE variable in the page_header.php that refer to a specific CSS named like the template. And you don't use it in your template! :-)
AT least, you can get the path to the css with PHPWG_ROOT_PATH.'template/'.$user['template'].

So I advise to either use only one CSS named as the template (as you first planned) or create a T_STYLE_PATH variable which leads to the template folder.

chrisaga has been working on this issue. He has separated templates and themes. For each template (like "yoga"), you can have multiple themes (clear, dark, and so on). First commit from chrisaga on this issue was [Subversion] r960

FIXME in header.tpl was deleted thanks to use of template variables : template/{themeconf:template}/default-layout.css